@jrss I haven't used the Emacs `diff`, but I use `ediff` heavily.
The following link (a really old blog post of mine) does not have ediff tips, but a "DWIM" wrapper around ediff functions so that I need to call just that one ediff-related binding :)
@kaushalmodi still not getting it from what I saw and your post. Seems like the regular emacs diff is good enough to compare org files...? Having hard time finding a video examples of how to use, etc.
@jrss From what I understand, ediff is more interactive. About the M-x diff, there is this in the manual: http://www.gnu.org/software/emacs/manual/html_node/emacs/Diff-Mode.html
@kaushalmodi tips about the Emacs one please :)